GenomicAnnotations-class: Class "GenomicAnnotations" to manage information about...

In PREDA: Position Related Data Analysis

Description

This class is used to manage information about genomic features under investigation: i.e. genomic genes, SNP or others, with particular focus on the genomic coordinates of each of them. Other additional annotations associated to each element can be stored in a GenomicAnnotations object in the optionalAnnotations slots

Objects from the Class

Objects can be created by calls of the form new("GenomicAnnotations", ids, chr, start, end, strand, chromosomesNumbers, chromosomesLabels, optionalAnnotations, optionalAnnotationsHeaders).

Slots

ids:

Object of class "character" ~~

chr:

Object of class "integer" ~~

start:

Object of class "integer" ~~

end:

Object of class "integer" ~~

strand:

Object of class "numeric" ~~

chromosomesNumbers:

Object of class "numeric" ~~

chromosomesLabels:

Object of class "character" ~~

optionalAnnotations:

Object of class "matrix" ~~

optionalAnnotationsHeaders:

Object of class "character" ~~

Methods

GenomicAnnotations2dataframe

signature(.Object = "GenomicAnnotations"): extracts annotations as a dataframe with probeids as rownames

GenomicAnnotations2GenomicAnnotationsForPREDA

signature(.Object = "GenomicAnnotations"): generate a new GenomicAnnotationsForPREDA object from a GenomicAnnotations object

GenomicAnnotations2reference_positions

signature(.Object = "GenomicAnnotations"): extract from the GenomicAnnotations object a vector containing a vector with reference positions

GenomicAnnotationsExtract

signature(.Object = "GenomicAnnotations"): extract optional annotations for a specific region

GenomicAnnotationsFilter_neg

signature(.Object = "GenomicAnnotations"): filter annotations to remove selected chromosomes

GenomicAnnotationsFilter_pos

signature(.Object = "GenomicAnnotations"): filter annotations to keep selected chromosomes

GenomicAnnotationsSortAndCleanNA

signature(.Object = "GenomicAnnotations"): sort annotations according to selected chromosomes and to remove genes containing any NA annotation field

GenomicRegionsAnnotate

signature(.Object1 = "GenomicRegions", .Object2 = "GenomicAnnotations"): extract annotations from a GenomicAnnotations object for a set of regions specified as a GenomicRegions object

initialize

signature(.Object = "GenomicAnnotations"): initialize method for GenomicAnnotations objects

Note

This class is better described in the package vignette

Author(s)

Francesco Ferrari

See Also

GenomicAnnotations2dataframe, GenomicAnnotations2GenomicAnnotationsForPREDA, GenomicAnnotations2reference_positions,GenomicAnnotationsExtract, GenomicAnnotationsFilter_neg,GenomicAnnotationsFilter_pos, GenomicAnnotationsSortAndCleanNA,GenomicRegionsAnnotate,

Examples

showClass("GenomicAnnotations")

PREDA documentation built on Nov. 8, 2020, 7:40 p.m.